GSE12680
GSE GEODivergent transcription from active promoters
Organism:
Mus musculus
Platform:
GPL9185
Samples:
1
Experiment Types:
Genome binding/occupancy profiling by high throughput sequencing
Submitted:
Sep 05 2008
Last Updated:
May 15 2019
Status:
Public on Dec 01 2008
Contact:
Stuart,,Levine (Whitehead Institute)
Relations
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP000627
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA112677
Summary
Here we describe a novel class of short RNAs and high-resolution ChIP-Seq data that together indicate widespread divergent transcription at mammalian promoters and suggest the existence of novel regulatory mechanisms concerning both initiation and elongation by RNA polymerase II.
Overall Design
ChIP-seq in murine embryonic stem cells for RNA polymerase II
Analysis (4 steps)
View Data Processing
Processing steps for GSE12680
- Images analysis and base calling was done using solexa pipeline and reads aligned to both mouse NCBI build 36 using ELAND.
- For ChIP-Seq, sequences from all lanes were extended 200bp (maximum fragment length accounting for ~100bp of primer sequence), and allocated into 25 bp bins.
- Genomic bins containing statistically significant ChIP-seq enrichment were identified by comparison to a Poissonian background model, using a p-value threshold of 10-9.
- Additionally, we used an empirical background model obtained from identical Solexa sequencing of DNA from whole cell extract (WCE) from matched cell samples (>5X normalized enrichment across the entire region).
GEO Samples (1)
Dataset Citations (1)
Divergent transcription from active promoters.
PMID 19056940
· 2008
· Science (New York, N.Y.)
Amy C Seila, J Mauro Calabrese, Stuart S Levine, Gene W Yeo, Peter B Rahl, Ryan A Flynn, Richard A Young, Phillip A Sharp
SRA Experiments (1) and Runs (1)
Total: 232 MBSample: SRS002256
BioProject: PRJNA112677
BioSample: SAMN00002074
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
cell type: V6.5 embryonic stem cells
chip antibody: RNAP2
strain: C57BL/6-129
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR014267 | 11562571 | 300626846 | 232.06 | mES_RNAP2_sequence.fastq, SRR014267, SRR014267.sralite | SRA |
Linked Publications (1)
Divergent transcription from active promoters.
Science (New York, N.Y.) · 2008
Data Files (1)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | mES_RNAP2_sequence.fastq | ChIP-Seq | 232.1 MB | link |